Locus 4285

Sequence ID	3R_DroMel_CAF1
Location	11,409,974 – 11,410,165
Length	191
Max. P	0.870289

overview

Window 9

Location	11,409,974 – 11,410,087
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.20
Mean single sequence MFE	-42.80
Consensus MFE	-36.34
Energy contribution	-36.58
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.38
Structure conservation index	0.85
SVM decision value	0.10
SVM RNA-class probability	0.582470
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11409974 113 + 27905053
CGGCGGUCCCGUGGGUAAAUUGAUAUUCCUGUCAUUGCUGUAAUGAUUUCUGCUUCCUGCGAUAGGAAUCGCGGUCCGGCGAUUGCCGUGUGC-------CGUGUAUCCUGGCGCAUCCU
(((((((((((.((((((..(((((....)))))))))).................(((((((....))))))).)))).))))))))(((((-------((.......))))))).... ( -39.20)
>DroSec_CAF1 157620 113 + 1
CGGCGGUCCCGUGGGUAAAUUGAUAUUCCUGUCAUUGCUGUAAUGAUUUCUGCUUCCUGCGGCAGGAAUCGCGGUCCGGCGAUUGCCGUGUGC-------CGUGUAUCCUGGCGCUUCCU
(((((((((((.((((((..(((((....)))))))))).....((((((((((......)))))))))).....)))).)))))))).((((-------((.......))))))..... ( -42.70)
>DroSim_CAF1 149088 113 + 1
CGGCGGUCCCGUGGGUAAAUUGAUAUUCCUGUCAUUGCUGUAAUGAUUUCUGCUUCCUGCGGCAGGAAUCGCGGUCCGGCGAUUGCCGUGUGC-------CGUGUAUCCUGGCGCAUCCU
(((((((((((.((((((..(((((....)))))))))).....((((((((((......)))))))))).....)))).))))))))(((((-------((.......))))))).... ( -43.90)
>DroEre_CAF1 145351 113 + 1
CGGCGGUCCCGUGGGUAAAUUGAUAUUCCUGUCAUUGCUGUAAUGAUUUCUGCUUCCUGCGGCAGGAACCGCGGUCCGGCGAUUGCCGUGUGC-------CGUGUAUCCUGGCGCAUCCU
.(((((...(((.(((((..(((((....))))))))))...)))....)))))...((((.(((((..(((((((((((....)))).).))-------))))..))))).)))).... ( -43.50)
>DroYak_CAF1 149208 120 + 1
CGGCGGUCCCGUGGGUAAAUUGAUAUUCCUGUCAUUGCUGUAAUGAUUUCUGCUUCCUGCGGCAGGAAUCGCGGUCCGGCGAUUGCCGUGUGCCGUAUGCCGUGUAUCCUGGCGCAUCCU
(((((((((((.((((((..(((((....)))))))))).....((((((((((......)))))))))).....)))).))))))))(((((((.((((...))))..))))))).... ( -44.70)
>consensus
CGGCGGUCCCGUGGGUAAAUUGAUAUUCCUGUCAUUGCUGUAAUGAUUUCUGCUUCCUGCGGCAGGAAUCGCGGUCCGGCGAUUGCCGUGUGC_______CGUGUAUCCUGGCGCAUCCU
(((((((((((.((((((..(((((....)))))))))).....((((((((((......)))))))))).....)))).)))))))).............((((......))))..... (-36.34 = -36.58 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	11,410,014 – 11,410,125
Length	111
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	91.30
Mean single sequence MFE	-39.42
Consensus MFE	-33.80
Energy contribution	-33.92
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.48
Structure conservation index	0.86
SVM decision value	0.87
SVM RNA-class probability	0.870289
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11410014 111 - 27905053
CCUGUCGCGGAUAGAAAAAAAAACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACG-------GCACACGGCAAUCGCCGGACCGCGAUUCCUAUCGCAGGAAGCAGAAAUCAUUA
((((((((((....................)))).)))))).((((((.(......))-------))...((((....))))..(((((((....))))).))..))).......... ( -36.25)
>DroEre_CAF1 145391 108 - 1
CCUGUCGCGGAUAGAAA-A--AACGACCAGCCGCAGGCAGGAUGCGCCAGGAUACACG-------GCACACGGCAAUCGCCGGACCGCGGUUCCUGCCGCAGGAAGCAGAAAUCAUUA
((((((((((.......-.--.........)))).)))))).((((.(((((..(.((-------(....((((....))))..))).)..))))).))))................. ( -40.93)
>DroYak_CAF1 149248 116 - 1
CCUGUCGCGGAUAGAAAAA--AACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACGGCAUACGGCACACGGCAAUCGCCGGACCGCGAUUCCUGCCGCAGGAAGCAGAAAUCAUUA
(((((.((((.........--.........)))).(((((((((((((.(......))))....((....((((....))))..)))))..))))))))))))............... ( -41.07)
>consensus
CCUGUCGCGGAUAGAAAAA__AACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACG_______GCACACGGCAAUCGCCGGACCGCGAUUCCUGCCGCAGGAAGCAGAAAUCAUUA
(((((.((((....................)))).(((((((..(((..(......).............((((....))))....)))..))))))))))))............... (-33.80 = -33.92 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	11,410,054 – 11,410,165
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.22
Mean single sequence MFE	-28.64
Consensus MFE	-22.34
Energy contribution	-22.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.78
SVM decision value	0.12
SVM RNA-class probability	0.593817
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11410054 111 - 27905053
UAAUCUCGAAGAAAAUGUUUGCCUUUCUUUAAUUCAAUAUCCUGUCGCGGAUAGAAAAAAA--AACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACG-------GCACACGGCAAUC
..................(((((..............(((((((((((((...........--.........)))).))))))))).(((.(......))-------))....))))).. ( -29.05)
>DroSec_CAF1 157700 113 - 1
UAAUCUCGAAGAAAAUGUUUGCCUUUCUUUAAUUCAAUAUCCUGUCGCGGAUAUAAAAAAAAGAACGACAAGCGGCAGGCAGGAAGCGCCAGGAUACACG-------GCACACGGCAAUC
..................(((((.........(((.....((((((((.......................))))))))...)))(.(((.(......))-------)).)..))))).. ( -25.30)
>DroSim_CAF1 149168 113 - 1
UAAUCUCGAAGAAAAUGUUUGCCUUUCUUUAAUUCAAUAUCCUGUCGCGGAUAGAAAAAAAAGAACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACG-------GCACACGGCAAUC
..................(((((..............(((((((((((((......................)))).))))))))).(((.(......))-------))....))))).. ( -28.95)
>DroEre_CAF1 145431 108 - 1
UAAUCUCGAAGAAAAUGUUUGCCUUUCUUUAAUUCAAUAUCCUGUCGCGGAUAGAAA-A----AACGACCAGCCGCAGGCAGGAUGCGCCAGGAUACACG-------GCACACGGCAAUC
..................(((((..............(((((((((((((.......-.----.........)))).))))))))).(((.(......))-------))....))))).. ( -29.43)
>DroYak_CAF1 149288 116 - 1
UAAUCUCGAAGAAAAUGUUUGCCUUUCUUUAAUUCAAUAUCCUGUCGCGGAUAGAAAAA----AACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACGGCAUACGGCACACGGCAAUC
...............(((.((((..............(((((((((((((.........----.........)))).))))))))).(((.(......))))....)))).)))...... ( -30.47)
>consensus
UAAUCUCGAAGAAAAUGUUUGCCUUUCUUUAAUUCAAUAUCCUGUCGCGGAUAGAAAAAAA__AACGACAAACCGCAGGCAGGAUGCGCCAGGAUACACG_______GCACACGGCAAUC
..................(((((..............(((((((((((((......................)))).))))))))).((..................))....))))).. (-22.34 = -22.74 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:42 2006